BTW, hardly needed for this project but want to put in a plug for a good product from a guy quite near to where I work.
http://www.jkdevices.com/arduino-megaminiWe're likely to be working closely with him on a mod to this platform, for our project.
We need the additional PWM pins. He says we could probably reduce the size to 1/4 of what you see there (if we eliminate unneeded analog and digitals). Not bad. In its stock form, you end up with a festoonage of headers. It's amazingly dense. It'll also sink a half amp (though we're feeding transistors for current's sake) with its regulator. He took a hint from me and is experimenting with a particular potting compound, just now, with thermal control in view for high current applications. It's an interesting alternative to heat sinks per se.
Geez the Arduino platform is fruitful in the market. Every time I turn around someone's using 'em for something, and the number (and quality!) of libraries is expanding ridiculously.
I might even improve my java skills by way of C.
I hafta admit, though, coding real-time stuff can be really tricky -- especially when you need to do periodic things in an analogy way. And that's all I'll say without an NDA in play.